May 16, 2019

Today’s digest includes the microbial communities of fruit peels, bacterial crude oil degradation, and the gut microbiome of sea cucumbers. Enjoy!

Pregnancy and early life

Preprint: Interactions between the gut microbiome and mucosal immunoglobulins A, M and G in the developing infant gut – Janzon – BioRxiv

Human gut microbiome

Evolution of the gut microbiome following acute HIV-1 infection – Rocafort – Microbiome

Animal microbiome

Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation – Yao – Evolutionary Bioinformatics

High-throughput sequencing of 16S rRNA amplicons characterizes gut microbiota shift of juvenile sea cucumber Apostichopus japonicus feeding with three antibiotics – Zhao – Journal of Oceanology and Limnology

Plant, root, and soil microbiome

Contrasting patterns and drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests – Chen – Applied Microbiology and Biotechnology

Evaluation of microbial communities in peels of Brazilian tropical fruits by amplicon sequence analysis – Cruz – Brazilian Journal of Microbiology

Assembly mechanisms of soil bacterial communities in subalpine coniferous forests on the Loess Plateau, China – Zhao – Journal of Microbiology

Evaluating the effects of canine urine on urban soil microbial communities – Lee – Urban Ecosystems

Methane emission and soil microbial communities in early rice paddy as influenced by urea-N fertilization – Liu – Plant and Soil

Rhizosphere carbon supply accelerates soil organic matter decomposition in the presence of fresh organic substrates – Jackson – Plant and Soil

The relative contributions of pH, organic anions, and phosphatase to rhizosphere soil phosphorus mobilization and crop phosphorus uptake in maize/alfalfa polyculture – Sun – Plant and Soil

Diversity of anammox bacteria and abundance of functional genes for nitrogen cycling in the rhizosphere of submerged macrophytes in a freshwater lake in summer – Zhao – Journal of Soils and Sediments

Direct and indirect effects of elevated CO2 and nitrogen addition on soil microbial communities in the rhizosphere of Bothriochloa ischaemum – Xiao – Journal of Soils and Sediments

Rhizocompartments and environmental factors affect microbial composition and variation in native plants – Kang – Journal of Microbiology

The inhibitory effect of cadmium and/or mercury on soil enzyme activity, basal respiration, and microbial community structure in coal mine–affected agricultural soil – Zheng – Annals of Microbiology

Water and extremophile microbiome

Preprint: Metabolic Architecture of the Deep Ocean Microbiome – Acinas – BioRxiv

Production of Current by Syntrophy Between Exoelectrogenic and Fermentative Hyperthermophilic Microorganisms in Heterotrophic Biofilm from a Deep-Sea Hydrothermal Chimney – Pillot – Microbial Ecology

A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups – Shurigin – MicrobiologyOpen

Molecular analyses of bacterioplankton communities with highly abundant Vibrio clades: a case study in Bohai Sea coastal waters – Wang – Journal of Oceanology and Limnology

Archaeal communities in the deep-sea sediments of the South China Sea revealed by Illumina high-throughput sequencing – Li – Annals of Microbiology

Bacterial succession and co‐occurrence patterns of an enriched marine microbial community during light crude oil degradation in a batch reactor – Uribe‐Flores – Journal of Applied Microbiology

Microbial assemblages reflect environmental heterogeneity in alpine streams – Hotaling – Global Change Biology

Food microbiology

Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal – Groenenboom – PLoS One

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March 27, 2019

Happy Wednesday! Today’s digest includes spider endosymbionts, microbes shared between family members, and the effects of plastic on the microbiome of compost. Enjoy!

General microbiome

Transmission of human-associated microbiota along family and social networks – Brito – Nature Microbiology

Diversity-disease relationships and shared species analyses for human microbiome-associated diseases – Ma – ISME

Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity – Fodelianakis – Nature Communications

Preprint: Exploring the archaeome: detection of archaeal signatures in the human body – Pausan – bioRxiv

Human gut microbiome

Sucrose 6F-phosphate phosphorylase: a novel insight in the human gut microbiome – Tauzin – Microbial Genomics

Human skin microbiome

Preprint: Moving microbes: the dynamics of transient microbial residence on human skin – Vandegrift – bioRxiv

Animal experiments

Effects of phycocyanin in modulating the intestinal microbiota of mice – Xie – MicrobiologyOpen

Animal microbiome

Preprint: Endosymbiotic bacteria are prevalent and diverse in agricultural spiders – White – bioRxiv

Plant, root, and soil microbiome

Litter Quality Modulates Effects of Dissolved Nitrogen on Leaf Decomposition by Stream Microbial Communities – Jabiol – Microbial Ecology

Additions of sugar and nitrogenous fertiliser affect plant nitrogen status and soil microbial communities – Morrow – Applied Soil Ecology

Characterizing differences in microbial community composition and function between Fusarium wilt diseased and healthy soils under watermelon cultivation – Wang – Plant and Soil

Meta-analysis shows positive effects of plant diversity on microbial biomass and respiration – Chen – Nature Communications

Effects of transgenic glufosinate-tolerant rapeseed (Brassica napus L.) and the associated herbicide application on rhizospheric bacterial communities – Tang – Physiological and Molecular Plant Pathology

Structure and Diversity of Soil Bacterial Communities in Offshore Islands – Lin – Scientific Reports

The effect of environment on the microbiome associated with the roots of a native woody plant under different climate types in China – Chen – Applied Microbiology and Biotechnology

Variation in rhizosphere priming and microbial growth and carbon use efficiency caused by wheat genotypes and temperatures – Yin – Soil Biology and Biochemistry

Using a soil bacterial species balance index to estimate potato crop productivity – Jeanne – PLoS One

Limited effect of planting transgenic rice on the soil microbiome studied by continuous 13CO2 labeling combined with high-throughput sequencing – Wang – Applied Microbiology and Biotechnology

Range-expansion effects on the belowground plant microbiome – Ramirez – Nature Ecology and Evolution

Water and extremophile microbiome

Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments – Marshall – ISME

Built environment

Exploring the long-term effect of plastic on compost microbiome – Esan – PLoS One

An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced “iron mound” sediments – Leitholf – PLoS One

Probiotics/prebiotics

Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling – Ansari – PLoS One

Review: Importance of probiotics in the prevention and treatment of colorectal cancer – Eslami – Journal of Cellular Physiology

Techniques

Robust sampling and preservation of DNA for microbial community profiling in field experiments – Groenenboom – BMC Research Notes

January 31, 2019

Today’s digest covers articles describing sphingolipids in host-microbiome interaction, unique microbiome and metabolome of Indian population, selection and stabilization of soil microbiome and effect of probiotics on early sepsis in patients and immune response in childrenEnjoy reading!

General microbiome

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview – Partho Sen – Metabolites

Altered composition and function of intestinal microbiota in autism spectrum disorders: a systematic review – Feitong Liu – Translational Psychiatry

Sphingolipids in host–microbial interactions – Stacey L. Heaver – Current Opinion in Microbiology

Pregnancy and early life

Mixed Viral-Bacterial Infections and Their Effects on Gut Microbiota and Clinical Illnesses in Children – Shilu Mathew – Scientific Reports

Pathways linking caesarean delivery to early health in a dual burden context: Immune development and the gut microbiome in infants and children from Galápagos, Ecuador – Amanda L. Thompson – American Journal of Human Biology

Human gut microbiome

The vagino-cervical microbiome as a woman’s life history – Zhuye Jie – BioRxiv

Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers – Nielson T. Baxter – mBio

The unique composition of Indian gut microbiome, gene catalogue and associated faecal metabolome deciphered using multi-omics approaches – D.B. Dhakan – Gigascience

Animal experiments

Oral neonatal antibiotic treatment perturbs gut microbiota and aggravates central nervous system autoimmunity in Dark Agouti rats – Suzana Stanisavljević – Scientific Reports

Intestinal epithelial N-acylphosphatidylethanolamine phospholipase D links dietary fat to metabolic adaptations in obesity and steatosis – Amandine Everard – Nature Communications

Mutual interplay between IL-17–producing γδT cells and microbiota orchestrates oral mucosal homeostasis – Anneke Wilharm – PNAS

Plant, root and soil microbiome

Selection, succession and stabilization of soil microbial consortia – Elias K. Zegeye – BioRxiv

Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow – Mohammad Ghashghavi – BioRxiv

Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance – Sammy Frenk – Applied and Environmental Microbiology

Water and extremophiles microbiome

Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity – Aleksei A. Korzhenkov – Microbiome

Antibiotic disturbance affects aquatic microbial community composition and foodweb interactions but not community resilience – Ester M. Eckert – Molecular Ecology

 Phages and viruses

Megaphages infect Prevotella and variants are widespread in gut microbiomes – Audra E. Devoto – Nature Microbiology

Probiotics / prebiotics

Dysbiosis in early sepsis can be modulated by a multispecies probiotic: a randomised controlled pilot trial – V. Stadlbauer – Beneficial Microbes

Lactobacillus plantarum IS-10506 supplementation increases faecal sIgA and immune response in children younger than two years – P.D. Kusumo – Beneficial Microbes

Supplementation with Lactobacillus kefiranofaciens ZW3 from Tibetan Kefir improves depression-like behavior in stressed mice by modulating the gut microbiota – Ye Sun – Food and Function

Non-microbiology picks

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping – Helmuth Gehart – Cell

December 14, 2018

The microbiota of chigger mites and praying mantids, the prevalence of thermophiles in domestic water heaters, the bacteria that colonize and degrade centuries-old art.

General microbiome

Migration alters oscillatory dynamics and promotes survival in connected bacterial populations – Shreyas Gokhale – Nature Communications

Pre-print: A probabilistic model to identify the core microbial community – Thiago Gumiere – bioRxiv

Human oral microbiome

Pre-print: Correlation between the oral microbiome and brain resting state connectivity in smokers – Dongdong Lin – bioRxiv

Animal experiments

Host-targeted niclosamide inhibits C. difficile virulence and prevents disease in mice without disrupting the gut microbiota – John Tam – Nature Communications

Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets – Ann-Sofie Riis Poulsen – PLOS ONE

Animal microbiome

Bacterial microbiome of the chigger mite Leptotrombidium imphalum varies by life stage and infection with the scrub typhus pathogen Orientia tsutsugamushi – Loganathan Ponnusamy – PLOS ONE

The hindgut microbiota of praying mantids is highly variable and includes both prey-associated and host-specific microbes – Kara A Tinker – PLOS ONE

Plant, root, and soil microbiome

Belowground fungal community diversity and composition associated with Norway spruce along an altitudinal gradient – Max E. Schön – PLOS ONE

Treating wheat seeds with neonicotinoid insecticides does not harm the rhizosphere microbial community – Yaofa Li – PLOS ONE

Water and extremophile microbiome

Pre-print: An archaeal symbiont-host association from the deep terrestrial subsurface – Katrin Schwank – bioRxiv

Marine-Derived Fungi: Promising Candidates for Enhanced Bioremediation – Anjana K Vala – Approaches in Bioremediation

Built environment

Biogeography of thermophiles and predominance of Thermus scotoductus in domestic water heaters – Regina L Wilpiszeski – Extremophiles

Probiotics/prebiotics

Dopamine production in Enterococcus faecium: A microbial endocrinology-based mechanism for the selection of probiotics based on neurochemical-producing potential – Daniel Villageliú – PLOS ONE

Phages and viruses

A chemical defence against phage infection – Sarah Kronheim – Nature

Bioinformatics

Pre-print: Metagenome-wide measurement of protein synthesis in the human fecal microbiota using MetaRibo-Seq – Brayon J Fremin – bioRxiv

Pre-print: Large-scale analyses of human microbiomes reveal thousands of small, novel genes and their predicted functions – Hila Sberro – bioRxiv

Metabolomics

Rumen and plasma metabolomics profiling by UHPLC-QTOF/MS revealed metabolic alterations associated with a high-corn diet in beef steers – You Yang – PLOS ONE

More microbes

Pre-print: Real-time capture of horizontal gene transfers from gut microbiota by engineered CRISPR-Cas acquisition – Christian Munck – bioRxiv

Bacteria art

A detailed look at the microorganisms that colonize, and degrade, a 400-year-old painting – ScienceDaily

Inside SAIC’s Bio Art Lab, where art is life—literally – Paul Dailing – Chicago Reader

Across China: Medical students paint “Mona Lisa” with bacteria – Xinhua Net

Science, career, and publishing

Pre-print: Non-academic employability of life science PhDs: the importance of training beyond the bench – Sohyoung Her – bioRxiv

October 24, 2018

General Microbiome

REVIEW:Leaky Gut, Leaky Brain? Obrenovich MEM. Microorganisms.

Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children.Chen B. International Immunopharmacology.

Airway microbiome is associated with respiratory functions and responses to ambient particulate matter exposure.Wang L. Ecotoxicology and Environmental Safety

Gut Microbiome

Association of serum bilirubin in newborns affected by jaundice with gut microbiota dysbiosis.Zhou S. The Journal of Nutritional Biochemistry

Author Correction: Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Zhernakova DV. Nature Genetics

Competitive lottery-based assembly of selected clades in the human gut microbiome.Verster AJ. Microbiome.

Vaginal Microbiome

Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study.Arokiyaraj S. Scientific Reports

Increased transferrin saturation is associated with subgingival microbiota dysbiosis and severe periodontitis in genetic haemochromatosis.Boyer E. Scientific Reports

Plant, Soil, and Water Microbiome

Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers.He Z. Environmental Pollution

Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters.Deja-Sikora E. Microbial Ecology

The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales.Li HY. Microbiome

Potential methane production and molecular characterization of bacterial and archaeal communities in a horizontal subsurface flow constructed wetland under cold and warm seasons. López D. The Science of the Total Environments

Biotechnological potential of plant growth-promoting bacteria from the roots and rhizospheres of endemic plants in ironstone vegetation in southeastern Brazil.Felestrino ÉB. World Journal of Microbiology and Biotechnology

Temporal shifts in endophyte bacterial community composition of sessile oak (<i>Quercus petraea</i>) are linked to foliar nitrogen, stomatal length, and herbivory. Borruso L. Peer

Shifts in community composition and co-occurrence patterns of phyllosphere fungi inhabiting <i>Mussaenda shikokiana</i> along an elevation gradient.Qian X. PeerJ.

Techniques

Protocol for faecal microbiota transplantation in ulcerative colitis (FMTUC): a randomised feasibility study.Jitsumura M. BMJ Open

September 24, 2018

General microbiology

Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine – Jason Merritt, PHYSICAL REVIEW LETTERS

Small at Size, Big at Impact: Microorganisms for Sustainable Development – Nasib Singh, Microbial Bioprospecting for Sustainable Development

Population Genomics of Archaea: Signatures of Archaeal Biology from Natural Populations – David J. Krause, Population Genomics

Pregnancy and early life

Sharing of human milk oligosaccharides degradants within bifidobacterial communities in faecal cultures supplemented with Bifidobacterium bifidum – Aina Gotoh, Scientific Reports

Multi-site human microbiome

Gut–Liver Axis: How Do Gut Bacteria Influence the Liver? – Peter Christopher Konturek, Medical Sciences

Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health – Kathrin Beyer, Plos One

Optimal immunosuppressor induces stable gut microbiota after liver transplantation – Jian-Wen Jiang, World Journal of Gastroenterology

Human respiratory microbiome

The Microbiome and Tuberculosis: Early Evidence for Cross Talk – Sivaranjani Namasivayam, mBio

Trans-maternal Helicobacter pylori exposure reduces allergic airway inflammation in offspring through regulatory T-cells – Andreas Kyburz, Journal of Allergy and Clinical Immunology

Human oral microbiome

Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situbiofilm model – Stefan Rupf, Scientific Reports

Human gut microbiome

In silico Identification of Metagenomic Signature Describing Neurometabolic Potential of Normal Human Gut Microbiota – A. S. Kovtun, Russian Journal of Genetics

Gut microbiota modulates drug pharmacokinetics – Juanhong Zhang, Drug Metabolism Reviews

Active Site Flexibility Revealed in Crystal Structures of Parabacteroides merdae β‐Glucuronidase from the Human Gut Microbiome – Michael S. Little, Protein Science

Structural and Functional Analysis of the Gut Microbiome for Toxicologists – Robert G. Nichols, Current Protocols in Toxicology

Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation – Sean M. P. Bennet, Neurogastroenterology and Motility

Animal experiments

Response of goose intestinal microflora to the source and level of dietary fiber – Haizhu Zhou, Poultry Science

Microbiota modulation by eating patterns, dietary and macronutrient composition; impact on food intake – Elizabeth A. Klingbeil, American Journal of Physiology

Water and extremophile microbiome

Accounting for bacterial overlap between raw water communities and contaminating sources improves the accuracy of signature-based microbial source tracking – Moa Hägglund, Frontiers in Microbiology

Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85–90 °N – Beatriz Fernández-Gómez, ISME

Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean – Francisco Martinez-Hernandez, ISME

Microbial Community Function in Electroactive Biofilm-based Constructed Wetlands – Ramírez Vargas, Biogeosciences

Fungal endophyte‐infected leaf litter alters in‐stream microbial communities and negatively influences aquatic fungal sporulation – Emily R. Wolfe, Synthesising Ecology

Salt marsh denitrification is impacted by oiling intensity six years after the Deepwater Horizon oil spill – Corianne Tatariw, Environmental Pollution

Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination – Blaise P. Bougnom, Environmental Research

Plant, root, and soil microbiome

Phosphate solubilizing bacteria with glucose dehydrogenase gene for phosphorus uptake and beneficial effects on wheat – Muhammad Suleman, Plos One

Multiple ecological processes jointly drive the soil microbial community assembly in subalpine coniferous forests – Pengyu Zhao, PeerJ

Aphid Colonization Affects Potato Root Exudate Composition and the Hatching of a Soil Borne Pathogen – Grace A. Hoysted, Frontiers in Plant Sciences

Root inoculation with Azotobacter chroococcum 76A enhances tomato plants adaptation to salt stress under low N conditions – Michael James Van Oosten, BMC Plant Biology

Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France) – Jorge R. Osman, Antonie van Leeuwenhoek

Plant roots alter microbial functional genes supporting root litter decomposition – Shengjing Shi, Soil Biology and Biochemistry

Bacterial community response to a preindustrial‐to‐future CO2 gradient is limited and soil‐specific in Texas Prairie grassland – Swastika Raut, Global Change Biology

Built environment

Houseplants as home health monitors – C. Neal Stewart Jr., SYNTHETIC BIOLOGY

Characterization of Aspergillus niger Isolated from the International Space Station – Jillian Romsdahl, mSystems

Food microbiology

Microbiological Changes during Ripening of Chihuahua Cheese Manufactured with Raw Milk and Its Seasonal Variations – Cristina Sánchez-Gamboa, Foods

Supplementation in mushroom crops and its impact on yield and quality – Jaime Carrasco, AMB Express

Aronia (Aronia melanocarpa) Polyphenols Modulate Microbial Community in Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) and Decrease Secretion of Pro‐Inflammatory Markers in a Caco‐2/endothelial Cell Co‐Culture Model – Ting Wu, Molecular Nutrition and Food Research

Techniques

A critical evaluation of the use of gas chromatography- and high performance liquid chromatography-mass spectrometry techniques for the analysis of microbial metabolites in human urine after consumption of orange juice – José Luis Ordóñez, Journal of Chromatography A

Recovering cellular biomass from fluids using chemical flocculation – Paul A. Kenward, Environmental Microbiology Reports

Influence of support media supplementation to reduce the inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics – Simon Poirier, Data in Brief

A resourceful methodology to profile indolic auxins produced by rhizo-fungi using spectrophotometry and HPTLC – Dhavalkumar Patel, Biotech

Bioinformatics

Computational Tools and Databases of Microbes and Its Bioprospecting for Sustainable Development – Dipannita Hazra, Microbial Bioprospecting for Sustainable Development

Metabolomics

Paradoxes in leaky microbial trade – Yoav Kallus, Nature Communications

Antibiotics

Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen – Gleb Pishchany, PNAS

Microbes in the news

Subculture show converts Storefront for Art and Architecture into living lab – The Architects Newspaper, Ali Oriaku

August 20, 2018

Happy Monday! Today’s Microbiome Digest is chock-full. You’ll find: a review of approaches towards predictive microbial ecology, insights into function gleaned from rumen metatranscriptomics, diet studies in hunter-gatherers and mice, characterization of the mosquito and termite microbiota, the wild side of plant microbiomes, fermentation for traditional liquors, and much more!

General microbiome
Systems biology approaches towards predictive microbial ecology – Anne E. Otwell – Environmental Microbiology

One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review – Pauline Trinh – Frontiers in Public Health

Tuning of human MAIT cell activation by commensal bacteria species and MR1-dependent T-cell presentation – Cihan Tastan – Mucosal Immunology

Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation – Andrea Söllinger – mSystems

Multi-site human microbiome
A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis – Shaheen Alanee – Prostate

Streptococcus and Prevotella are associated with the prognosis of oesophageal squamous cell carcinoma – Yanfang Liu – Journal of Medical Microbiology

Urinary symptoms are associated with certain urinary microbes in urogynecologic surgical patients – Cynthia S. Fok – International Urogynecology Journal

Human gut microbiome
Links between environment, diet, and the hunter-gatherer microbiome – Gabriela K. Fragiadakis – Gut Microbes

Klebsiella oxytoca expands in cancer cachexia and acts as a gut pathobiont contributing to intestinal dysfunction – Sarah A. Pötgens – Scientific Reports

Co-Administration of Probiotics with Prescribed Antibiotics for Preventing Clostridium difficile Diarrhea – Ahmed S. I. Hamed – Academic Emergency Medicine

Animal experiments
Effect of industrial trans-fatty acids-enriched diet on gut microbiota of C57BL/6 mice – Yueting Ge – European Journal of Nutrition

AIEC infection triggers modification of gut microbiota composition in genetically predisposed mice, contributing to intestinal inflammation – Alexis Bretin – Scientific Reports

Effect of probiotic Bifidobacterium bifidum G9-1 on the relationship between gut microbiota profile and stress sensitivity in maternally separated rats – Hirokazu Fukui – Scientific Reports

Animal microbiome
Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype – Dawn B. Goldsmith – Scientific Reports

Neonatal gut and immune maturation is determined more by postnatal age than by post-conceptional age in moderately preterm pigs – Shuqiang Ren – American Journal of Physiology-Gastrointestinal and Liver Physiology

Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite –  Ning Liu – ISME Journal

Mosquito microbiota cluster by host sampling location – Ephantus J. Muturi – Parasites and Vectors

Plant, root, and soil microbiome|
The wild side of plant microbiomes – Juan E. Pérez-Jaramillo – Microbiome

Unraveling the Composition of the Root-Associated Bacterial Microbiota of Phragmites australis and Typha latifolia – Laura Pietrangelo – Frontiers in Microbiology

Vermicompost addition influences symbiotic fungi communities associated with leek cultivated in metal-rich soils – Antoine Pierart – Environmental Science and Pollution Research

Plant drought resistance is mediated by soil microbial community structure and soil-plant feedbacks in a savanna tree species – Nianxun Xi – Environmental and Experimental Botany

Metabolic specialization of denitrifiers in permeable sediments controls N2 O emissions – Hannah K. Marchant – Environmental Microbiology

Bacterial Biomarkers of Marcellus Shale Activity in Pennsylvania – Jeremy R. Chen See – Frontiers in Microbiology

Eighteen-Year Farming Management Moderately Shapes the Soil Microbial Community Structure but Promotes Habitat-Specific Taxa – Huaihai Chen – Frontiers in Microbiology

Water and extremophile microbiome
Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments – José Q. García-Maldonado – Extremophiles

Subsurface landfill leachate contamination affects microbial metabolic potential and their expression in the Banisveld aquifer – Neslihan Taş – FEMS Microbiology Ecology

Food microbiology
Robust Domination of Lactobacillus sakei in Microbiota During Traditional Japanese Sake Starter Yamahai-Moto Fermentation and the Accompanying Changes in Metabolites – Atsushi Tsuji – Current Microbiology

DaQu fermentation selects for heat resistant Enterobacteriaceae and bacilli – Zhiying Wang – Applied and Environmental Microbiology

Exploitation of autochthonous Tuscan sourdough yeasts as potential starters – Michela Palla – International Journal of Food Microbiology

Techniques
Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria – Tamaki Ito – Gut Microbes